Was he on a big-arse dose of flagyl? When we thought my boys may have had giardia or a cryptospridium from the water, they were on a super high dosage (6-250 pills a day). We sent off to some super high-tech lab that did flourescent stains and nothing showed for the giardia or cryptospridium. We then went to a round of sulfasalazine for colitis, because at that point, their guts were totally messed up (we had blood in poo for weeks). We ran a round of that, and I changed foods. Mind you, I am not a person who likes change, and I don't change foods. Anyway, we have determined since that it had to be the food. The boys have had very limited treats, the new kibble, and a homecooked for an add in. If I try to throw in anything different, I see Chase looking a little punky. I think in the reading I did, it said we needed a totally different protein and carb source, and the duration would be at least three months to start, and maybe six months. Unfortunately, I had already bought the food and stayed with chicknen , which is the meat source we use here. The boys did get better, so we had to figure it was the original kibble. We also threw in some probiotics along the way, after the flagyl. I then used some acidolpholous for for Chase for about a week.
So, as I see it, his gut is messed up big time, and he has an additional stressor of being in a new place. I think you have some really good suggestions from the others who have responded. I hope he starts to mend soon. He'll be awhile healing up and getting back to normal considering where he is now.
Good luck